Questions tagged [molecular-structure]

This tag should be applied to questions that deal with the particular arrangement of atoms in a molecule, the so-called molecular structure or geometry.

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What make elements toxic in one molecule and nontoxic in another

Please excuse my seemingly silly question, I am just trying to understand this point. My question is about chemistry. I will use phenol as an example only. Phenol is indicated to be toxic. The ...
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Enantiomers or identical structures?

What is the relationship between the following pair of molecules? Is the underlined answer correct? Explain. I'm getting mixed answers. Some say these are identical molecules. Other say these are ...
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Why do PBr3 and PCl3 have larger bond angles than PH3?

According to the Colby Chemistry Database, the bond angle of $\ce{PBr3}$ and $\ce{PCl3}$ are around $101$ degrees, but the bond angle of $\ce{PH3}$ is $92$ degrees. (Source: PCl3 PBr3 PH3) There was ...
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Molecular Orbital Diagram

Chemists have revealed that $1 \lambda^{2}, 2 \lambda^{2}$ -disilene $\left(\mathrm{Si}_{2}\right)$ is diamagnetic while disulfur $\left(\mathrm{S}_{2}\right)$ is paramagnetic $(\mathrm{S}=1)$. Draw ...
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Why do both bonding and antibonding molecular orbitals exist at the same time when two waveforms could only be in-phase or out-of-phase? [closed]

I am quite confused concerning the existence of both bonding and antibonding molecular orbitals. I understand from previous posts that the number of orbitals has to be conserved, and thus when two ...
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Net direction of dipole moment in oxygen difluoride

What is the net direction of dipole moment in $\ce{F2O}$ molecule? In the case of $\ce{NH3}$ and $\ce{NF3}$ molecules both have net dipole moment with direction reversed due to strong ...
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What does “the natural bond angle” mean in the context of Universal Force Field (UFF) potential energy calculation and how are bond angles calculated?

As the title says, what does "the natural bond angle θ0" mean in the context of Universal Force Field (UFF) potential energy calculation? The reference appears in section D. Angular ...
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Why does dilithium have a longer bond length than dihydrogen?

I've tried MO theory however they both have a bond order of 1. Which means we can not relate the bond order to the bond length. My thinking - I think that the h2 bond length is shorter due to only ...
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Does anyone know what program was used to make this molecular structure picture? [closed]

I am a quantum chemistry beginer, and this picture color scheme is classic. I wonder how to make such pictures by myself.
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Why is the shape of sulphates and perchlorates such that lattice enthalpy doesn't decrease down the group? [duplicate]

The solubility of carbonates, bicarbonates and hydroxides of s-block elements increases down the group. But, the solubility of their sulphates and perchlorates decreases down the group. The reason for ...
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Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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Why is the dihedral angle of solid hydrogen peroxide less than that of gaseous? [duplicate]

Hydrogen peroxide has an "open book" structure: The dihedral angle in gaseous H$_2$O$_2$ is close to what we might expect in a tetrahedral arrangement. However, in solid H$_2$O$_2$ it's ...
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Diatomic molecule under pressure

If we put a diatomic molecule under pressure the interatomic distance will be decreased and according to this graph the potential energy of the bonding molecular orbital will be increased. What will ...
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1answer
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Are there square planar complexes with sp2d hybridization?

We were taught (Under the section 'Valence Bond Theory') seven types of geometries a transition metal complex may assume and its corresponding hybridization states, Linear - $\ce{sp}$ Trigonal planar ...
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Why is the methyl radical planar?

Why is the methyl radical planar? The VSEPR theory would predict an angle between 120° and 109.5°, while it is actually 120°.
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Structure-Activity Relationship of Chlormephos and Parathion

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/k. ...
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Identification of the organic compound

An organic compound A $(\ce{C10H14O})$ exhibits following characteristics. A) It reacts with metallic sodium to give a colorless odorless gas. B) It is oxidized by $\ce{KMnO4}$ to benzoic acid. C) It ...
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Comparing O−O bond length in hydrogen peroxide and dioxide(2−) ion

Problem How can we qualitatively compare the bond lengths between $\ce{H2O2}$ and $\ce{O2^2-}?$ Answer Attempt I tried using molecular orbital theory, but since both have peroxide $\ce{O2^2-},$ the ...
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Are phenyl and allyl groups in prop-2-enylbenzene coplanar?

Wouldn't C1 and C2 in prop-2-enylbenzene be on the same plane as that of the phenyl ring, right? If the double bond connected to C2 was between it and C1, they would be, but is it correct that now ...
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Is selenium disulfide polar or non-polar?

So I saw in some internet site that $\ce{SeS2}$ is a polar molecule. When I drew the Lewis structure of the molecule, it showed up as a linear molecule like this: $$\ce{S=Se=S}$$ The electronegativity ...
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1answer
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Can molecule have just h-bonds between its parts

I'm just starting to study chemistry so sorry for the probably obvious question to you, guys. According to the definition of molecule in Wikipedia: A molecule is an electrically neutral group of two ...
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Convergence issue in Gaussian

I have been struggling with geometry optimization of a prostaglandin molecule (20 carbon atoms). I finally got the optimization, all right. Then I did the Frequency job on the optimized structure (I ...
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1answer
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How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?

Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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Help understanding how “steric effects” are distinct from “electronic effects”?

@jakebeal's excellent answer to Why do animal cells “mistake” rubidium ions for potassium ions? includes the following passage: In the case of potassium versus sodium, which are both very important ...
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Deciding which group twists out of the plane when ortho effect takes place

I'm going to take a few stills from 3D conformers of the following compounds available on PubChem in which ortho effect is applicable to show what I'm referring to. 2-Nitrobenzoic acid: N,N-Dimethyl-...
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Change of ionic packing upon crystals are pressurized

When rock salt crystal is pressurized, its FCC structure changes to BCC structure whereby coordination ratio changes from 6:6 to 8:8. At the same time packing efficiency of the crystal decreases from ...
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How are there two C3 rotation axes in ammonia?

If we look at the character table for the $C_\mathrm{3v}$ point group (which $\ce{NH3}$ is an example of), we see that these are the symmetry elements ${E, 2 C_3, 3 \sigma_v}$ present in the molecule. ...
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Is N--O--N known to exist?

Commonly, the empirical formula $\ce{N2O}$ refers to the molecule with structure $\ce{N\bond{~--}N\bond{~-}O}$. Is the isomer $\ce{N-O-N}$ known to exist? I'm guessing it is significantly less stable ...
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What is the 3D shape of an ethane molecule?

I am currently teaching a course on groups, and want to give my students "real life" examples of symmetry groups to think about. The ethane molecule would be one such. But, the on-line ...
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Why is T-shaped geometry preferred to trigonal planar geometry for the bonds around atoms with 3 bonds and 2 lone pairs?

This is regarding a situation where an atom has five electron domains; two domains are lone pairs, and three are bonds to other atoms. The course materials I am using (focusing on VSEPR theory) ...
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Porous materials: Is the expression of a mean free path $\overline{\ell}$ of the gas molecule valid for a binary mixtures?

Suppose that I have a binary gas mixture at low pressure. Can I calculate the mean free path $\overline{\ell}$ of the gas molecule in a pores of solid material by substituting a molecular weight of a ...
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286 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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Identifying the molecular structure of compound with sum formula C8H14O3 formula using NMR and IR spectrometry data

I am looking to identify the molecular structure of a compound with the sum formula $\ce{C8H14O3}$ using the NMR and IR spectrometry data below. I was able to figure out the molecule as My friend ...
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1answer
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Lack of elaboration in IR spectra of compounds

I've recently started learning about IR spectroscopy, and a common trend I'm seeing in my textbook and other sources is that not all the features in the IR spectrum are explained in detail. The focus ...
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1answer
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ATP chemical structure: phosphate groups with Oxygen anions or with OH groups?

I've googled repeatedly (with multiple search queries) to try and get an answer to this question but nothing comes up. Embarrassingly, I seem to be the only person who is confused by: ATP with oxygen ...
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Is azonine planar?

I came across aza[9]-annulene, which is given to be aromatic. I can clearly see it follows Hückel's rule with 8 π-electrons in the ring and the lone pair of nitrogen. But the thing that concerns me ...
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Geometries of SCl2(OCH3)2 and SF2(OCH3)2

I am not able to understand the difference between structure of $\ce{SCl_{2}(OCH_{3})_{2}}$ and $\ce{SF_{2}(OCH_{3})_{2}}$. I am already well versed with Molecular Orbital and VSEPR theories. I found ...
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How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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Energy levels of combined orbitals

I saw the MO diagram for a NH3 molecule but couldn't understand why the combined atomic orbitals were in the positions they were, and if these positions were fixed. Why is the sigma anti bonding ...
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How to use Google’s Alpha-fold to predict a two-protein complex?

Alpha-fold won the CASP13 and CASP14 competitions last year and this year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence. Google has ...
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What is the geometry of a tri-substituted methyl free radical?

My teacher explained that free radicals could have a geometry that is planar or pyramidal(tending to tetrahedral) based on whether or not it is substituted by lone-pair containing atoms. For example, $...
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Convert an image of a chemical structure to a ChemDraw file?

Is there a way to convert a bitmap (JPG, PNG) image of a chemical structure to a ChemDraw file so that you don't have to draw a structure you find in a paper yourself?
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Is it rigorous enough to change a DFT functional after geometry optimization to calculate excited state properties?

I have done the geometry optimization with the B3LYP functional, however, there is a need to calculate the excited state energy, so the CAM-B3LYP functional should be better suited for that. Do I need ...
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Do changing opt=modredundant to opt in Gaussian makes geometry optimization not to take into account frozen angles?

I am a newbie to Gaussian and just generated an input for the geometry optimization for some molecules with multi ring system. However, in the article that was a reference for those calculations, some ...
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If all bond angles in AX₃ are the same, then which of the following are correct conclusions about AX₃?

Question If all bond angles in $\ce{AX3}$ are the same, then which of the following are correct conclusions about $\ce{AX3}?$ (A) $\ce{AX3}$ must be polar. (B) $\ce{AX3}$ must be planar. (C) $\ce{AX3}...
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How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does. By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
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2answers
316 views

What is intermolecular distance in water? [closed]

I am wondering what is an average intermolecular distance in liquid water (say under normal pressure and room temperature). I need just order of magnitude. A reference would be helpful.
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How can I determine the size of tropolone molecule?

How can I determine the size of a tropolone molecule? It's a seven-membered aromatic ring with =O on the first carbon and -OH on the second carbon. Is there any software available?
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What does a filled, solid circle mean in a chemical structure?

I'm looking in a textbook at an asphaltene molecule. The two aromatic rings next to the Nitrogen are shaded. What does that mean? I think the Nitrogen's create delocalized electrons in this ...
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Does the non-serotonin-like half of LSD resemble anything of significance?

LSD's resemblance to serotonin explains many of its effects on the brain, but I noticed only half of it resembles serotonin. The question I have, is does the other half resemble anything, particularly ...

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